Added documentation and header information for AMOEBA 2013 force field

docs/usersguide/application.rst

@@ -660,7 +660,9 @@ amber99sbildn.xml  AMBER99SB plus improved side chain torsions\ :cite:`Lindorff-
 amber99sbnmr.xml   AMBER99SB with modifications to fit NMR data\ :cite:`Li2010`
 amber03.xml        AMBER03\ :cite:`Duan2003`
 amber10.xml        AMBER10
-amoeba2009.xml     AMOEBA\ :cite:`Ren2002`                                                       
+amoeba2009.xml     AMOEBA 2009\ :cite:`Ren2002`.  This force field is deprecated.  It is 
+                   recommended to use AMOEBA 2013 instead.
+amoeba2013.xml     AMOEBA 2013\ :cite:`Shi2013`
 =================  ================================================================================
 
 
@@ -692,15 +694,16 @@ the following files:
 
 .. tabularcolumns:: |l|L|
 
-=================  ==============================================================================================
+=================  =================================================================================================
 File               Implicit Solvation Model                                                                      
-=================  ==============================================================================================
+=================  =================================================================================================
 amber96_obc.xml    GBSA-OBC solvation model\ :cite:`Onufriev2004` for use with AMBER96 force field
 amber99_obc.xml    GBSA-OBC solvation model for use with AMBER99 force fields
 amber03_obc.xml    GBSA-OBC solvation model for use with AMBER03 force field
 amber10_obc.xml    GBSA-OBC solvation model for use with AMBER10 force field
-amoeba2009_gk.xml  Generalized Kirkwood solvation model\ :cite:`Schnieders2007` for use with AMOEBA force field
-=================  ==============================================================================================
+amoeba2009_gk.xml  Generalized Kirkwood solvation model\ :cite:`Schnieders2007` for use with AMOEBA 2009 force field
+amoeba2013_gk.xml  Generalized Kirkwood solvation model for use with AMOEBA 2013 force field
+=================  =================================================================================================
 
 
 For example, to use the GBSA-OBC solvation model with the Amber99SB force field,

docs/usersguide/references.bib

@@ -336,10 +336,20 @@
    type = {Journal Article}
 }
 
+@article{Shi2013
+   author = {Shi, Yue and Xia, Zhen and Zhang, Jiajing and Best, Robert and Wu, Chuanjie and Ponder, Jay W. and Ren, Pengyu},
+   title = {Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins},
+   journal = {Journal of Chemical Theory and Computation},
+   volume = {9},
+   number = {9},
+   pages = {4046-4063},
+   year = {2013},
+   type = {Journal Article}
+}
+
 @article{Shirts2007
    author = {Shirts, Michael R. and Mobley, David L. and Chodera, John D. and Pande, Vijay S.},
-   title = {Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular
-Simulations},
+   title = {Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations},
    journal = {Journal of Physical Chemistry B},
    volume = {111},
    pages = {13052-13063},

wrappers/python/simtk/openmm/app/data/amoeba2013.xml

-<!-- Generated on 2014-03-11 from amoebapro13.prm -->
-
 <ForceField>
+ <Info>
+  <Source>amoebapro13.prm</Source>
+  <DateGenerated>2014-03-11</DateGenerated>
+  <Reference>Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, and Pengyu Ren. Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation, 9(9):4046–4063, 2013.</Reference>
+ </Info>
  <AtomTypes>
   <Type name="1" class="1" element="N" mass="14.007"/>
   <Type name="2" class="2" element="C" mass="12.011"/>

wrappers/python/simtk/openmm/app/data/amoeba2013_gk.xml

-<!-- Generated on 2014-03-11 from amoebapro13.prm -->
-
 <ForceField>
+ <Info>
+  <Source>amoebapro13.prm</Source>
+  <DateGenerated>2014-03-11</DateGenerated>
+  <Reference>Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, and Pengyu Ren. Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation, 9(9):4046–4063, 2013.</Reference>
+ </Info>
  <AmoebaGeneralizedKirkwoodForce solventDielectric="78.3" soluteDielectric="1.0" includeCavityTerm="1" probeRadius="0.14" surfaceAreaFactor="-170.351730663">
   <GeneralizedKirkwood type="1" charge="-0.22483" shct="0.79"  /> 
   <GeneralizedKirkwood type="2" charge="-0.09722" shct="0.72"  />